A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes
Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2018-12-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e29.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832574082535653376 |
|---|---|
| author | Min-Jung Kim Si-Cho Kim Young-Joon Kim |
| author_facet | Min-Jung Kim Si-Cho Kim Young-Joon Kim |
| author_sort | Min-Jung Kim |
| collection | DOAJ |
| description | Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments. |
| format | Article |
| id | doaj-art-18a73cccf6c14fc5867a21776f21dabe |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-18a73cccf6c14fc5867a21776f21dabe2025-02-02T00:52:08ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e29531A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular IndexesMin-Jung Kim0Si-Cho Kim1Young-Joon Kim2 Department of Integrated Omics and Biomedical Science, Yonsei University, Seoul 03722, Korea Department of Biochemistry, Yonsei University, Seoul 03722, Korea Department of Integrated Omics and Biomedical Science, Yonsei University, Seoul 03722, KoreaHybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.http://genominfo.org/upload/pdf/gi-2018-16-4-e29.pdfhybrid captureprecision medicinetargeted sequencingunique molecular indexvariant calling |
| spellingShingle | Min-Jung Kim Si-Cho Kim Young-Joon Kim A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes Genomics & Informatics hybrid capture precision medicine targeted sequencing unique molecular index variant calling |
| title | A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes |
| title_full | A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes |
| title_fullStr | A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes |
| title_full_unstemmed | A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes |
| title_short | A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes |
| title_sort | universal analysis pipeline for hybrid capture based targeted sequencing data with unique molecular indexes |
| topic | hybrid capture precision medicine targeted sequencing unique molecular index variant calling |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e29.pdf |
| work_keys_str_mv | AT minjungkim auniversalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes AT sichokim auniversalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes AT youngjoonkim auniversalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes AT minjungkim universalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes AT sichokim universalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes AT youngjoonkim universalanalysispipelineforhybridcapturebasedtargetedsequencingdatawithuniquemolecularindexes |